# This file is part of POMAShiny.

# POMAShiny is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# POMAShiny is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with POMAShiny. If not, see <https://www.gnu.org/licenses/>.

fluidRow(
  column(width = 3,
         
         box(
           width = 12,
           inputId = "volcano_card",
           title = "Volcano plot parameters",
           status = "primary",
           solidHeader = FALSE,
           collapsible = FALSE,
           collapsed = FALSE,
           closable = FALSE,
           
           selectInput("pval", "p-value type", choices = c("raw", "adjusted"), selected = "raw"),
           
           numericInput("pval_cutoff", strong("p-value threshold"), value = 0.05, step = 0.01),
           
           numericInput("log2FC", strong("log2 Fold change threshold"), value = 1.5, step = 0.1),
           
           numericInput("xlim", "x-axis range", value = 2),
           
           prettySwitch("paired_vol", "Paired samples", fill = TRUE, status = "primary"),
           
           prettySwitch("var_equal_vol", "Equal variance", fill = TRUE, status = "primary") %>% helper(type = "markdown",
                                                                                                       title = "Volcano plot helper",
                                                                                                       content = "volcano",
                                                                                                       icon = "question",
                                                                                                       colour = "green")
           
         )
         ),
  
  column(width = 9,
         
         plotlyOutput("vocalnoPlot", height = "500px")

         )
  )

